If I remove the battery in my 1998 Accord, does it effect the ECU in any way?

I'm not understanding - if you remove the battery from the vehicle -- disconnect the battery -- it will definitely reset any "memory" the engine's processor has, resetting all parameters to a basic level that will require the engine's processor to "relearn" once the engine is started again after battery reconnection.

Idle strategy ay be affected but that will take care of itself upon next engine operation. Just pay attention to battery POLARITY.